I don't "think" an exhaust leak would cause a big enough harmonic noise in the block to trip the knock sensor. 95 EFI does have a knock sensor in one of the block drain plugs.
If you ran it again with the exh leak and not running rough it may have just been an anomoly that it ran rough the first time.
You dont say which gasket. Manifold to head or manifold to riser?
Mike is correct on the riser gasket could potentially be blown out on the inside surface as well and allow water into the dry side of the exhaust.
If it's the gasket on the head then run it as long as it's not a big exhaust leak, maybe leave the blower on, think CO2 in the engine box.
Either way it's theoratically a simple fix save for every exhaust seems to have stubborn rusty bolts that wont come out or break.
I'd park it and start hitting the bolts with penetrating oil. Trick to getting out rusty exhaust bolts. If you can heat up the portion that the boltis threaded into head or manifold and not the bolt per se, with a cutting torch (even Mapp gas will work but will take alot longer) you can usually remove the bolt easily because the piece the bolt is threaded into expands slightly braking the rust bond in the threads.

__________________
'06 X2 MCX

"I understand why some people may not want to do this the way I have recommended but I can't understand the death grip some people have on a toilet plunger with a hose fitting." -JimN

Did you pull all plugs to make sure water is not getting into the cylinder from a leaking riser gasket? I think you really want to rule that out. Hydro lock is a bad thing. Just went through this on a buddies Malibu. He got lucky and only blew the head gasket. It was a knocking noise like you describe and still ran (though roughly). Just something to consider.

It is the gasket on the head. My manifold to riser gaskets are seeping but not leaking like crazy or anything.

Maybe the sound with the cover down tripped the knock sensor. The problem is on the port side.

My knock sensor is original. So Rockman I might take you up on that

We did hook it up to see if any codes were thrown and nothing at all came up.

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Ok, let me know. I replaced mine last fall and this was the one that came with the boat when we bought it last fall...it worked fine, no issues, but just wanted to replace it as the outer looks of it was worn.

Replace the gasket. $25ish for the gasket and bolts plus an hour or two.

As mentioned, you will want to check the mating and wall thickness. When I had my leak, we found how pitted the faces and thin the walls had become. Knocking off some of the rust further up the elbow showed how close they were getting to allowing water into the cylinders.

So, what I am saying is, fix the easy leak but go in knowing there is a decent chance you will be forking out $300 a side for new exhaust and risers.